# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 21:21:43 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(CC#C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(C)C1=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 RYA  RYA  (7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one  ligand  41  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RYA
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 RYA  C4   C  CR66  0   0.190  -2.1419  -1.2165  -0.0557
 RYA  C14  C  CR16  0  -0.514   3.1143  -0.7994  -0.0840
 RYA  C5   C  CR6   0   0.601   0.1753   0.0834   0.2198
 RYA  C6   C  CR16  0  -0.065  -0.9279  -1.8282  -0.2474
 RYA  C11  C  CR6   0   0.490   4.9295   1.2171   0.3967
 RYA  C9   C  CR6   0   0.387   2.6507   0.4681   0.2669
 RYA  C10  C  CR16  0  -0.534   3.5856   1.4814   0.5088
 RYA  C12  C  CR6   0   0.044   5.4316  -0.0317   0.0480
 RYA  C13  C  CR6   0   0.507   4.4753  -1.0075  -0.1805
 RYA  N1   N  NR6   0  -0.497  -3.2670   0.8170   0.4536
 RYA  N2   N  NR6   0  -0.569  -3.3707  -1.8797  -0.0790
 RYA  C3   C  CR66  0   0.543  -2.0927   0.1568   0.2682
 RYA  N3   N  N     0  -0.510  -0.9464   0.7847   0.4120
 RYA  C1   C  CR6   0   0.574  -4.5328  -1.1890  -0.1878
 RYA  C2   C  CR16  0  -0.220  -4.4019   0.3276  -0.3339
 RYA  N4   N  N     0  -0.484   0.2393  -1.1896  -0.1200
 RYA  O1   O  O     0  -0.463  -5.6189  -1.7345  -0.2191
 RYA  N5   N  NH1   0  -0.778   1.3153   0.8137   0.3985
 RYA  O2   O  OH1   0  -0.622   6.7630  -0.2087  -0.0414
 RYA  F1   F  F     0  -0.321   4.9165  -2.2325  -0.5204
 RYA  C16  C  CSP1  0  -0.515  -2.8530   3.7348  -1.4161
 RYA  C17  C  CH3   0  -0.696  -5.7043   1.0099   0.0423
 RYA  H1   H  HCR6  0   0.312   2.4341  -1.6128  -0.2787
 RYA  H2   H  HCR6  0   0.287  -0.8644  -2.8796  -0.5008
 RYA  H3   H  HCH3  0   0.258  -2.7187  -3.6744   0.7697
 RYA  H4   H  HCH3  0   0.278  -4.3841  -3.6786   0.1816
 RYA  H5   H  HCH3  0   0.257  -3.0490  -3.7631  -0.9704
 RYA  H6   H  HCH2  0   0.310  -4.1137   2.5337   1.2703
 RYA  H7   H  HCH2  0   0.310  -2.3856   2.3968   1.4631
 RYA  H8   H  HCR6  0   0.296   3.2668   2.4786   0.7863
 RYA  H9   H  HCR6  0   0.286  -4.2128   0.5166  -1.4026
 RYA  H10  H  HNH1  0   0.412   1.1372   1.7755   0.6436
 RYA  H11  H  HOH1  0   0.479   6.9710  -1.1132  -0.3013
 RYA  H12  H  H     0   0.284  -2.7146   4.3300  -2.2895
 RYA  H13  H  HCH3  0   0.251  -5.6770   2.0706  -0.2002
 RYA  H14  H  HCH3  0   0.266  -6.5205   0.5748  -0.5277
 RYA  H15  H  HCH3  0   0.247  -5.9265   0.8962   1.1033
 RYA  C7   C  CH3   0  -0.558  -3.3788  -3.3297  -0.0252
 RYA  C8   C  CH2   0  -0.472  -3.1998   2.2339   0.7588
 RYA  F2   F  F     0  -0.310   5.8118   2.1969   0.6305
 RYA  C15  C  CSP   0   0.257  -2.9984   3.0658  -0.4284

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 RYA  F2   C11  single    1.339  0.020  1.339
 RYA  N4   C6   aromatic  1.337  0.020  1.337
 RYA  N4   C5   aromatic  1.319  0.020  1.319
 RYA  C10  C11  aromatic  1.374  0.020  1.374
 RYA  C10  C9   aromatic  1.400  0.020  1.400
 RYA  N5   C5   single    1.366  0.020  1.366
 RYA  N5   C9   single    1.386  0.020  1.386
 RYA  C6   C4   aromatic  1.373  0.020  1.373
 RYA  C11  C12  aromatic  1.390  0.020  1.390
 RYA  C5   N3   aromatic  1.337  0.020  1.337
 RYA  C9   C14  aromatic  1.394  0.020  1.394
 RYA  C7   N2   single    1.451  0.020  1.451
 RYA  C4   N2   single    1.396  0.020  1.396
 RYA  C4   C3   aromatic  1.412  0.020  1.412
 RYA  C12  O2   single    1.346  0.020  1.346
 RYA  C12  C13  aromatic  1.385  0.020  1.385
 RYA  N3   C3   aromatic  1.315  0.020  1.315
 RYA  C14  C13  aromatic  1.380  0.020  1.380
 RYA  N2   C1   single    1.356  0.020  1.356
 RYA  C3   N1   single    1.360  0.020  1.360
 RYA  C13  F1   single    1.346  0.020  1.346
 RYA  C1   O1   double    1.216  0.020  1.216
 RYA  C1   C2   single    1.529  0.020  1.529
 RYA  N1   C2   single    1.466  0.020  1.466
 RYA  N1   C8   single    1.451  0.020  1.451
 RYA  C2   C17  single    1.518  0.020  1.518
 RYA  C8   C15  single    1.464  0.020  1.464
 RYA  C15  C16  triple    1.202  0.020  1.202
 RYA  C14  H1   single    0.929  0.020  1.085
 RYA  C6   H2   single    0.929  0.020  1.085
 RYA  C7   H3   single    0.939  0.020  1.096
 RYA  C7   H4   single    0.939  0.020  1.096
 RYA  C7   H5   single    0.939  0.020  1.096
 RYA  C8   H6   single    0.939  0.020  1.096
 RYA  C8   H7   single    0.939  0.020  1.096
 RYA  C10  H8   single    0.929  0.020  1.085
 RYA  C2   H9   single    0.939  0.020  1.096
 RYA  N5   H10  single    0.868  0.020  1.013
 RYA  O2   H11  single    0.832  0.020  0.971
 RYA  C16  H12  single    0.913  0.020  1.066
 RYA  C17  H13  single    0.939  0.020  1.096
 RYA  C17  H14  single    0.939  0.020  1.096
 RYA  C17  H15  single    0.939  0.020  1.096

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 RYA  C3   C4   N2   119.76  3.000
 RYA  C3   C4   C6   115.76  3.000
 RYA  N2   C4   C6   124.35  3.000
 RYA  H1   C14  C13  119.72  3.000
 RYA  H1   C14  C9   121.43  3.000
 RYA  C13  C14  C9   118.85  3.000
 RYA  N5   C5   N4   120.62  3.000
 RYA  N5   C5   N3   113.64  3.000
 RYA  N4   C5   N3   125.73  3.000
 RYA  H2   C6   N4   115.77  3.000
 RYA  H2   C6   C4   121.12  3.000
 RYA  N4   C6   C4   123.10  3.000
 RYA  F2   C11  C12  117.58  3.000
 RYA  C12  C11  C10  123.12  3.000
 RYA  F2   C11  C10  119.30  3.000
 RYA  N5   C9   C10  116.53  3.000
 RYA  N5   C9   C14  124.82  3.000
 RYA  C10  C9   C14  118.65  3.000
 RYA  H8   C10  C9   120.94  3.000
 RYA  H8   C10  C11  119.07  3.000
 RYA  C9   C10  C11  119.99  3.000
 RYA  O2   C12  C13  125.40  3.000
 RYA  C13  C12  C11  115.13  3.000
 RYA  O2   C12  C11  119.47  3.000
 RYA  F1   C13  C12  117.16  3.000
 RYA  F1   C13  C14  118.57  3.000
 RYA  C12  C13  C14  124.26  3.000
 RYA  C2   N1   C3   115.68  3.000
 RYA  C2   N1   C8   118.36  3.000
 RYA  C3   N1   C8   117.57  3.000
 RYA  C1   N2   C7   120.47  3.000
 RYA  C1   N2   C4   120.89  3.000
 RYA  C7   N2   C4   118.61  3.000
 RYA  N3   C3   N1   120.40  3.000
 RYA  N1   C3   C4   118.26  3.000
 RYA  N3   C3   C4   121.33  3.000
 RYA  C3   N3   C5   117.73  3.000
 RYA  O1   C1   C2   121.26  3.000
 RYA  C2   C1   N2   116.07  3.000
 RYA  O1   C1   N2   122.62  3.000
 RYA  H9   C2   C17  108.10  3.000
 RYA  H9   C2   C1   106.11  3.000
 RYA  C17  C2   C1   110.41  3.000
 RYA  H9   C2   N1   109.33  3.000
 RYA  C17  C2   N1   112.41  3.000
 RYA  C1   C2   N1   110.25  3.000
 RYA  C6   N4   C5   116.32  3.000
 RYA  H10  N5   C9   115.55  3.000
 RYA  H10  N5   C5   113.23  3.000
 RYA  C9   N5   C5   131.20  3.000
 RYA  H11  O2   C12  110.78  3.000
 RYA  H12  C16  C15  180.00  3.000
 RYA  H15  C17  H14  108.41  3.000
 RYA  H15  C17  H13  108.88  3.000
 RYA  H14  C17  H13  106.99  3.000
 RYA  H15  C17  C2   111.68  3.000
 RYA  H14  C17  C2   109.55  3.000
 RYA  H13  C17  C2   111.19  3.000
 RYA  H5   C7   H4   108.53  3.000
 RYA  H5   C7   H3   108.88  3.000
 RYA  H4   C7   H3   108.72  3.000
 RYA  H5   C7   N2   111.29  3.000
 RYA  H4   C7   N2   109.50  3.000
 RYA  H3   C7   N2   109.87  3.000
 RYA  H7   C8   H6   106.41  3.000
 RYA  H7   C8   C15  109.68  3.000
 RYA  H6   C8   C15  109.87  3.000
 RYA  H7   C8   N1   108.47  3.000
 RYA  H6   C8   N1   109.19  3.000
 RYA  C15  C8   N1   113.01  3.000
 RYA  C16  C15  C8   180.00  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 RYA  CONST_01  C5   N4   C6   C4      0.00   0.0  0
 RYA  CONST_02  C5   N3   C3   C4      0.00   0.0  0
 RYA  CONST_03  C11  C10  C9   C14     0.00   0.0  0
 RYA  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 RYA  CONST_05  N3   C5   N4   C6      0.00   0.0  0
 RYA  CONST_06  N3   C3   C4   C6      0.00   0.0  0
 RYA  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 RYA  CONST_08  C12  C13  C14  C9      0.00   0.0  0
 RYA  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 RYA  CONST_10  C13  C14  C9   C10     0.00   0.0  0
 RYA  CONST_11  N4   C6   C4   C3      0.00   0.0  0
 RYA  CONST_12  N4   C5   N3   C3      0.00   0.0  0
 RYA  CONST_13  C2   C1   N2   C4      0.00   0.0  0
 RYA  CONST_14  O2   C12  C13  C14   180.00   0.0  0
 RYA  CONST_15  N5   C5   N4   C6    180.00   0.0  0
 RYA  CONST_16  N5   C9   C10  C11   180.00   0.0  0
 RYA  CONST_17  F1   C13  C12  C11   180.00   0.0  0
 RYA  CONST_18  F2   C11  C10  C9    180.00   0.0  0
 RYA  CONST_19  F1   C13  C14  C9    180.00   0.0  0
 RYA  CONST_20  O2   C12  C11  C10   180.00   0.0  0
 RYA  CONST_21  F2   C11  C12  C13   180.00   0.0  0
 RYA  CONST_22  N5   C9   C14  C13   180.00   0.0  0
 RYA  CONST_23  N5   C5   N3   C3    180.00   0.0  0
 RYA  CONST_24  O1   C1   N2   C4    180.00   0.0  0
 RYA  CONST_25  C2   C1   N2   C7    180.00   0.0  0
 RYA  CONST_26  H8   C10  C9   C14   180.00   0.0  0
 RYA  CONST_27  H2   C6   N4   C5    180.00   0.0  0
 RYA  CONST_28  H1   C14  C9   C10   180.00   0.0  0
 RYA  CONST_29  O1   C1   N2   C7      0.00   0.0  0
 RYA  Var_01    C2   N1   C3   C4    -31.02  30.0  1
 RYA  Var_02    C1   N2   C4   C6   -164.81  30.0  1
 RYA  Var_03    C5   N5   C9   C14    -0.99  30.0  2
 RYA  Var_04    N4   C5   N5   C9      1.12  30.0  2
 RYA  Var_05    C15  C8   N1   C3     80.52  30.0  3
 RYA  Var_06    H3   C7   N2   C4     47.49  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 RYA  chir_01  C2  C1  N1  C17  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 RYA  plan-1  C14  0.020
 RYA  plan-1  C11  0.020
 RYA  plan-1  C9   0.020
 RYA  plan-1  C10  0.020
 RYA  plan-1  C12  0.020
 RYA  plan-1  C13  0.020
 RYA  plan-1  N5   0.020
 RYA  plan-1  O2   0.020
 RYA  plan-1  F1   0.020
 RYA  plan-1  H1   0.020
 RYA  plan-1  H8   0.020
 RYA  plan-1  F2   0.020
 RYA  plan-2  C4   0.020
 RYA  plan-2  C5   0.020
 RYA  plan-2  C6   0.020
 RYA  plan-2  N1   0.020
 RYA  plan-2  N2   0.020
 RYA  plan-2  C3   0.020
 RYA  plan-2  N3   0.020
 RYA  plan-2  N4   0.020
 RYA  plan-2  N5   0.020
 RYA  plan-2  H2   0.020
 RYA  plan-3  C4   0.020
 RYA  plan-3  N2   0.020
 RYA  plan-3  C1   0.020
 RYA  plan-3  C2   0.020
 RYA  plan-3  O1   0.020
 RYA  plan-3  C7   0.020

